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<h2><a name="GeneralConcepts"></a>General Concepts</h2>

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<p><span class="keyword">DataWarrior</span> is a multi-purpose data analysis tool.
It works on any kind of tabular data assuming rows to contain objects or cases and
columns to contain associated properties and values.
<span class="keyword">DataWarrior</span> provides interactive views to visualize data,
to discover correlations and to extract hidden knowledge from large data sets.
Data filters allow focusing on specific data subsets in a dynamic way.
Chemical intelligence is woven into the program to work with chemical structures
as easily as with numerical values. Data can be filtered on structural motives,
views are chemistry aware, molecule properties can be predicted from chemical structures, and
specialized cheminformatics methods explore the relationship between chemical structure
and measured properties.
<span class="keyword">DataWarrior</span> supports multiple files types and allows
merging data from files with data from the clipboard or from databases.
<span class="keyword">DataWarrior</span> is freely available for Linux, Macintosh and Windows.<br>
This section explains general concepts and defines important keywords.</p>
<br>
<h3><a name="MainAndDetailViews"></a>Main View Area and Detail Area</h3>
<p>The <span class="keyword">Main View Area</span> shows one or multiple
<span class="keyword">Main Views</span>, everyone displaying data rows either as data table,
in a 2- or 3-dimensional interactive chart, or in another kind of view.
Typically, multiple <span class="keyword">Main Views</span> show the same (sub-)set of data,
but display the data in different ways. Multiple <span class="keyword">Main Views</span>
can coexist either stacked on top of each other
or side by side.</p>
<p align="center"><img src="help/img/basics/viewAreas.jpeg"></p>
<p>Individual <span class="keyword">Main Views</span> can be maximized or closed by clicking the respective
buttons on the view's header area. A right mouse click within the header area
opens a popup menu allowing to create new views or to create pictures of the view.
<span class="keyword">Main Views</span> can be moved to another position
by dragging its header area to the middle or any edge of another view.</p>
<p>While <span class="keyword">Main Views</span> show multiple rows, the <span class="keyword">Detail Area</span>
displays the content of one row in detail. 
When moving the mouse over a <span class="keyword">Main View</span> the <span class="keyword">Detail Area</span> 
is constantly updated to reveal the details of the row or marker underneath the mouse pointer.</p>
<br>
<h3>Table View</h3>
<p> The <span class="keyword">Table View</span> serves as a direct window to
the data contained in a <span class="keyword">DataWarrior</span> file. Through it
rows can be sorted, data of individual cells can be modified, and display options
for individual columns can be changed. The <span class="keyword">Table View</span>
cannot be removed nor can there be more than one <span class="keyword">Table View</span>.
Columns may display non-alpha-numerical content like molecules or reactions. The column
order may be changed and less important columns may be hidden. A column specific popup
menu is accessible from the column header.
<a href="help/views.html#TableView">More...</a></p>
<p align="center"><img src="help/img/basics/tableView.jpeg"></p>

<br>
<h3>2D-View</h3>
<p> This view visualizes table data in a 2-dimensional chart, e.g. as a scatter plot,
bar or pie chart, box plot, etc. It is dynamically linked with the <span class="keyword">Detail Area</span>
such that a mouse movement above the view updates the row's details according to the mouse 
position. Marker colors, shapes, and sizes are customizable and may depend on 
a column of your data. A right mouse click inside of the view reveals a popup menu
allowing to customize view settings. The <span class="menu">xyz</span> button in the view's
header area opens a popup with controls for assigning data columns and to dynamically zoom into each axis. 
<a href="help/views.html#2DAnd3DViews">More...</a></p>
<p align="center"><img src="help/img/basics/2dviews.jpeg"></p>
<br>
<h3>3D-View</h3>
<p> The <b>3D-View</b> is similar to the 2D-View, however, it displays markers or bars
in a three dimensional cartesian coordinate system. The left mouse button can be
used to select row markers or to change the <span class="keyword">Current Row</span>. Pressing and dragging
the right mouse button over empty space rotates the view. Pressing the same mouse button over a marker
opens a popup menu for changing view specific settings.
<a href="help/views.html#2DAnd3DViews">More...</a></p>
<br>
<h3>Form View</h3>
<p>
<span class="keyword">Form Views</span> present your data like a book with one page per data row.
A <span class="keyword">Design Mode</span> allows to custom tailor the form layout and
an <span class="keyword">Edit Mode</span> allows to directly manipulate the data shown.
<span class="keyword">Form Views</span> are particularly useful, if some table cells reference
html or picture detail information. Such detail information is not shown in the
<span class="keyword">Table View</span>. Instead the <span class="keyword">Table View</span>
displays a small number in a colored square indicating that more information is available.
<a href="help/views.html#FormView">More...</a>
</p>
<p align="center"><img src="help/img/basics/formView.jpeg"></p>
<br>

<h3><a name="Filters"></a>Filters</h3>
<p>
Filters may hide rows from main views to temporarily focus on the remaining visible rows.
Various filter kinds are available, but they all share certain characteristics.
Filters always apply to all views, i.e. remove the same rows from all views at the same time.
Filters can be inverted by selecting the inversion button. If a row is excluded by one or
more filters, then is is not visible in any view.
The status panel displays the number of visible rows, of the selected rows, and of all rows.
</p>
<p>The available filter types are:</p>
<table class="wspace">
  <tbody>
    <tr>
      <td class="wspace"><p><img src="help/img/basics/sliders.jpeg"></p></td>
      <td class="wspace"><span class="keyword">Sliders</span> filter rows based on numerical 
      or date values. They define an allowed or forbidden data range by defining 
      minimum and maximum values. Pressing the <span class="menu">Ctrl</span> 
      key while dragging the slider caps reduces sensitivity by a factor of 20 
      to allow fine-tuning.</td>
    </tr>
    <tr>
      <td class="wspace"><p><img src="help/img/basics/textFilter.jpeg"></p></td>
      <td class="wspace"><span class="keyword">Text filters</span> may be used to hide rows which match or don't match 
      a query string in a definable way. For advanced text pattern matching one 
      may define a <a class="links" href="help/regex.html">regular expression</a> with 
      the <span class="menu">matches regex</span> option.</td>
    </tr>
    <tr>
      <td class="wspace"><p><img src="help/img/basics/categories.jpeg"></p></td>
      <td class="wspace"><b>Category</b> filters hide certain categories of the data. Rows are 
      hidden if they don't belong to any of the checked categories. If some rows 
      belong to multiple categories at the same time, then a &lt;multiple categories&gt; 
      option is offered. If this is checked then rows belonging into multiple 
      categories are kept from hiding.</td>
    </tr>
    <tr>
      <td class="wspace"><p><img src="help/img/basics/categoryBrowser.jpeg"></p></td>
      <td class="wspace">A <span class="keyword">Category Browser</span> allows to quickly browse
      through the different categories within a dataset. This can be done stepwise
      through clicking the 'previous' and 'next' buttons or more rapidly by dragging the slider.
	</td>
    </tr>
    <tr>
      <td class="wspace"><p><img src="help/img/basics/listFilter.jpeg"></p></td>
      <td class="wspace"><b>Row List</b> filters are used to hide all
      members of a
      selected hitlist or all rows that do not belong to that hitlist.</td>
    </tr>
    <tr>
      <td class="wspace"><p><img src="help/img/basics/structureFilter.jpeg"></p></td>
      <td class="wspace">Chemical <span class="keyword">structure filters</span> may be used to 
      show or hide compounds with a given substructure or that are similar to a 
      given molecule. <a href="help/chemistry.html#StructureFilter">More...</a><br>
      </td>
    </tr>
    <tr>
      <td class="wspace"><p><img src="help/img/basics/sssList.jpeg"></p></td>
      <td class="wspace">Two specialized filters allow an immediate filtering based on multiple
      structures at once. The <span class="keyword">SSS list filters</span> run a parallel
      sub-structure-search on multiple query structures and hides rows, whose molecules
      don't contain any of the listed query fragments. Fragment lists can be
      loaded from file, edited manually or combined by drag and drop.
      </td>
    </tr>
    <tr>
      <td class="wspace"><p><img src="help/img/basics/simList.jpeg"></p></td>
      <td class="wspace"><span class="keyword">Similarity structure list filters</span> may be used to 
      hide rows, whose molecules are not similar to any of the listed structures.
      Any currently available descriptor may serve as similarity criterion.
      </td>
    </tr>
  </tbody>
</table>

<p>Depending on the data, <span class="keyword">DataWarrior</span> shows 
a reasonable set of default filters. One can always add more filters or remove 
filters from the filter panel. Multiple active filters accumulate their affects, which 
means that rows are hidden if they don't match the filter condition of at least 
one filter.</p>

<br>
<h3><i><a name="VisibleRows"></a>Visible Rows</i></h3>
<p> The <span class="keyword">Visible Rows</span> are those rows, which are
currently visible in the main view area. Typically the set of <span class="keyword">
Visible Rows</span> is a subset of all rows of the dataset. Its number is always
displayed in the status area. The visibility of rows is primarily affected by filter
settings. However, a visible main view may also hide some rows,
e.g. through zooming or if the data row has empty values. This usually hides effected rows from other
visible views as well, unless the hiding view is configured to not contribute to global
row hiding. Main views, which are hidden behind other views, don't contribute to global row hiding.
Thus, the number of <span class="keyword">Visible Rows</span> may change when main views change visibility.</p>

<br>
<h3><a name="SelectedRows"></a>Selected Rows</h3>
<p>All main views except for the <span class="keyword">Form View</span> allow to select
or deselect rows with the mouse. The row selection is shared among all views. Thus,
when you change the row selection in one view, the selection in all other views is
updated simultaniously. The number of (visible) selected rows is always displayed in the status area.</p>

<br>
<h3><a name="CurrentRow"></a>Current Row</h3>
<p>With a mouse click one row can be defined as the <span class="keyword">Current Row</span>.
As with the <span class="keyword">Selected Rows</span>, the <span class="keyword">Current Row</span>
is shared among all views. Most views mark the <span class="keyword">Current Row</span> with a
<b> <font color="#FF0000">red frame</font></b> or show it in <b><font color="#FF0000">red color</font></b>. 
The <span class="keyword">Form View</span> always shows the <span class="keyword">Current Row</span>.
Various display modes use the <span class="keyword">Current Row</span> as a reference to compare to
when using color to show similarities or when constructing neighbourship graphs, etc.</p>

<br>
<h3><a name="RowLists"></a>Row Lists</h3>
<p> A <span class="keyword">Row List</span> is a named subset of all rows.
<span class="keyword">Row Lists</span> may be used for various purposes in DataWarrior,
e.g. as subject of a filter, to affect marker sizes, shapes or colors, to highlight a group of rows,
to permanently store a current selection, to define data subset for a data analysis method, etc.
Defined <span class="keyword">Row Lists</span> are automatically saved within DataWarrior files.
The <span class="menu">List</span> menu contains functionality to create and
manipulate <span class="keyword">Row Lists</span>. You may for instance create a few
<span class="keyword">Row Lists</span> from different sets of selected rows and afterwards
add more rows to some of those lists with the <span class="menu">Add Selected To</span> item
from the <span class="menu">List</span> menu. This way one may manually assign rows to self
defined categories. Alternatively, one may add individual rows to a list by pressing the right mouse
button on any row in any view and selecting the respective list name from the
<span class="menu">Add Row To List</span> popup menu item.
<br>
The <span class="menu">Add Column From Row Lists...</span> menu creates a new table column
that contains for every row the names of all lists, which it is a member of. This
way list membership can be materialized and used for filtering, view customization, or
other purposes.</p>
<br>

<h3><a name="Templates"></a>Templates</h3>
<p> A <span class="keyword">Template</span> comprises all <span class="keyword">DataWarrior</span>
display settings. It includes the information about existing views and their orientation,
all view specific settings like marker colors, font sizes, shown labels etc. It contains information about active
filters and their settings, column aliases and about the layout of existing form views.
<span class="keyword">Templates</span> are part of a native <span class="keyword">DataWarrior</span>
file and may also be stored as a stand-alone file to be later re-applied to another similar or updated data set.
Templates may also be associated with a database query, such that query results are immediately shown
in a predefined way.</p>

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